Tube1 (tubulin, epsilon 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Tube1 (tubulin, epsilon 1) Rattus norvegicus
Analyze
Symbol: Tube1
Name: tubulin, epsilon 1
RGD ID: 1306048
Description: Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization and mitotic cell cycle. Predicted to be active in cytoplasm and microtubule. Orthologous to human TUBE1 (tubulin epsilon 1); INTERACTS WITH 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: epsilon-tubulin 1; LOC361856; tubulin epsilon chain
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82044,105,405 - 44,124,947 (+)NCBIGRCr8
mRatBN7.22042,552,390 - 42,570,324 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2042,552,437 - 42,570,314 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2044,301,332 - 44,319,212 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02043,960,540 - 43,978,422 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02044,691,131 - 44,711,392 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02044,220,823 - 44,238,830 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2044,220,840 - 44,238,830 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02045,947,839 - 45,965,854 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42043,280,097 - 43,298,415 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12043,303,212 - 43,320,224 (+)NCBI
Celera2043,268,759 - 43,287,021 (+)NCBICelera
Cytogenetic Map20q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)
microtubule  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Tube1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82044,105,405 - 44,124,947 (+)NCBIGRCr8
mRatBN7.22042,552,390 - 42,570,324 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2042,552,437 - 42,570,314 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2044,301,332 - 44,319,212 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02043,960,540 - 43,978,422 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02044,691,131 - 44,711,392 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02044,220,823 - 44,238,830 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2044,220,840 - 44,238,830 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02045,947,839 - 45,965,854 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42043,280,097 - 43,298,415 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12043,303,212 - 43,320,224 (+)NCBI
Celera2043,268,759 - 43,287,021 (+)NCBICelera
Cytogenetic Map20q12NCBI
TUBE1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386112,070,663 - 112,087,482 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6112,070,663 - 112,087,529 (-)EnsemblGRCh38hg38GRCh38
GRCh376112,391,866 - 112,408,685 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366112,498,673 - 112,515,349 (-)NCBINCBI36Build 36hg18NCBI36
Build 346112,498,674 - 112,515,349NCBI
Celera6113,133,162 - 113,150,058 (-)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6109,966,689 - 109,983,618 (-)NCBIHuRef
CHM1_16112,654,200 - 112,671,087 (-)NCBICHM1_1
T2T-CHM13v2.06113,254,081 - 113,270,900 (-)NCBIT2T-CHM13v2.0
Tube1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391039,009,946 - 39,035,863 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1039,009,972 - 39,028,538 (+)EnsemblGRCm39 Ensembl
GRCm381039,133,949 - 39,151,058 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1039,133,976 - 39,152,542 (+)EnsemblGRCm38mm10GRCm38
MGSCv371038,853,829 - 38,870,864 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361038,823,442 - 38,839,618 (+)NCBIMGSCv36mm8
Celera1040,018,252 - 40,035,260 (+)NCBICelera
Cytogenetic Map10B1NCBI
cM Map1020.16NCBI
Tube1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555264,484,128 - 4,501,709 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555264,484,867 - 4,519,603 (+)NCBIChiLan1.0ChiLan1.0
TUBE1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25132,086,778 - 132,103,650 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16129,974,988 - 129,991,860 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06109,881,084 - 109,898,086 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16113,956,404 - 113,973,416 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6113,953,575 - 113,973,403 (-)Ensemblpanpan1.1panPan2
TUBE1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11268,499,435 - 68,514,127 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1268,499,525 - 68,514,648 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1268,317,764 - 68,332,960 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01269,380,998 - 69,396,227 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1269,381,003 - 69,396,201 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11268,740,495 - 68,755,703 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01268,578,009 - 68,593,213 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01268,905,013 - 68,920,199 (-)NCBIUU_Cfam_GSD_1.0
Tube1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946103,518,756 - 103,551,162 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936679751,701 - 783,296 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TUBE1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl178,018,433 - 78,048,406 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1178,018,113 - 78,048,466 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2187,688,125 - 87,717,319 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TUBE1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11361,768,981 - 61,785,273 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1361,769,047 - 61,784,525 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604034,104,774 - 34,121,076 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tube1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462500718,003 - 47,592 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462500717,991 - 48,970 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tube1
394 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:798
Count of miRNA genes:326
Interacting mature miRNAs:421
Transcripts:ENSRNOT00000047194
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203161428444396023Rat

Markers in Region
RH129238  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22042,569,551 - 42,569,759 (+)MAPPERmRatBN7.2
Rnor_6.02044,237,734 - 44,237,941NCBIRnor6.0
Rnor_5.02045,964,758 - 45,964,965UniSTSRnor5.0
RGSC_v3.42043,297,319 - 43,297,526UniSTSRGSC3.4
Celera2043,285,925 - 43,286,132UniSTS
RH 3.4 Map20460.5UniSTS
Cytogenetic Map20q12UniSTS
AI577391  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.42043,297,942 - 43,298,063UniSTSRGSC3.4
Celera2043,286,548 - 43,286,669UniSTS
RH 3.4 Map20463.4UniSTS
Cytogenetic Map20q12UniSTS
AI013034  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22042,570,720 - 42,570,846 (+)MAPPERmRatBN7.2
Rnor_6.02044,238,903 - 44,239,028NCBIRnor6.0
Rnor_5.02045,965,927 - 45,966,052UniSTSRnor5.0
RGSC_v3.42043,298,488 - 43,298,613UniSTSRGSC3.4
Celera2043,287,094 - 43,287,219UniSTS
RH 3.4 Map20463.3UniSTS
Cytogenetic Map20q12UniSTS
AI577391  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22042,570,174 - 42,570,296 (+)MAPPERmRatBN7.2
Rnor_6.02044,238,357 - 44,238,478NCBIRnor6.0
Rnor_5.02045,965,381 - 45,965,502UniSTSRnor5.0
RGSC_v3.42043,297,942 - 43,298,063UniSTSRGSC3.4
Celera2043,286,548 - 43,286,669UniSTS
RH 3.4 Map20463.4UniSTS
Cytogenetic Map20q12UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 22 14 8 6 8 57 18 30
Low 3 21 43 33 13 33 8 11 17 17 11 11 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000047194   ⟹   ENSRNOP00000044143
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2042,552,437 - 42,570,314 (+)Ensembl
Rnor_6.0 Ensembl2044,220,840 - 44,238,830 (+)Ensembl
RefSeq Acc Id: NM_001399016   ⟹   NP_001385945
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82044,107,029 - 44,124,939 (+)NCBI
mRatBN7.22042,552,406 - 42,570,316 (+)NCBI
RefSeq Acc Id: XM_006256529   ⟹   XP_006256591
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82044,107,092 - 44,124,947 (+)NCBI
mRatBN7.22042,552,440 - 42,570,316 (+)NCBI
Rnor_6.02044,221,068 - 44,238,506 (+)NCBI
Rnor_5.02045,947,839 - 45,965,854 (+)NCBI
Sequence:
RefSeq Acc Id: XR_010060729
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82044,105,405 - 44,121,953 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_006256591   ⟸   XM_006256529
- Peptide Label: isoform X1
- UniProtKB: A6KIF6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000044143   ⟸   ENSRNOT00000047194
RefSeq Acc Id: NP_001385945   ⟸   NM_001399016
Protein Domains
Tubulin/FtsZ 2-layer sandwich   Tubulin/FtsZ GTPase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZRL5-F1-model_v2 AlphaFold D3ZRL5 1-400 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701649
Promoter ID:EPDNEW_R12173
Type:multiple initiation site
Name:Tube1_1
Description:tubulin, epsilon 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02044,220,873 - 44,220,933EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306048 AgrOrtholog
BioCyc Gene G2FUF-3478 BioCyc
Ensembl Genes ENSRNOG00000000598 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000047194 ENTREZGENE
  ENSRNOT00000047194.4 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.600 UniProtKB/TrEMBL
  3.40.50.1440 UniProtKB/TrEMBL
InterPro Epsilon_tubulin UniProtKB/TrEMBL
  Tub_FtsZ_C UniProtKB/TrEMBL
  Tubulin UniProtKB/TrEMBL
  Tubulin/FtsZ_2-layer-sand-dom UniProtKB/TrEMBL
  Tubulin/FtsZ_GTPase_sf UniProtKB/TrEMBL
  Tubulin_C UniProtKB/TrEMBL
  Tubulin_CS UniProtKB/TrEMBL
  Tubulin_FtsZ_GTPase UniProtKB/TrEMBL
KEGG Report rno:361856 UniProtKB/TrEMBL
NCBI Gene 361856 ENTREZGENE
PANTHER Tubulin UniProtKB/TrEMBL
  TUBULIN EPSILON CHAIN UniProtKB/TrEMBL
Pfam Tubulin UniProtKB/TrEMBL
  Tubulin_C UniProtKB/TrEMBL
PhenoGen Tube1 PhenoGen
PRINTS EPSLNTUBULIN UniProtKB/TrEMBL
  TUBULIN UniProtKB/TrEMBL
PROSITE TUBULIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000598 RatGTEx
SMART Tubulin UniProtKB/TrEMBL
  Tubulin_C UniProtKB/TrEMBL
Superfamily-SCOP Tub_FtsZ_C UniProtKB/TrEMBL
  Tubulin_FtsZ UniProtKB/TrEMBL
UniProt A6KIF3_RAT UniProtKB/TrEMBL
  A6KIF6 ENTREZGENE, UniProtKB/TrEMBL
  D3ZRL5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-11-11 Tube1  tubulin, epsilon 1  Tube1  epsilon-tubulin 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Tube1  epsilon-tubulin 1  Tube1_predicted  tubulin, epsilon 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Tube1_predicted  tubulin, epsilon 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED